For 3.0, I have a short wishlist. If anyone at Apple is reading this (I doubt it, but who knows :) ), please consider the following things:
Speed / responsiveness
The biggest concerns for me about Aperture is the speed. Image loading is quite slow (for a 12MP RAW of my Canon EOS 450D on a 1 year-old MacBook Pro takes about 2-3 seconds), plus if I do some retouching, and I accidentally have to undo, it takes ages to re-render the photo.
If the software need to generate previews or thumbnails, it becomes really slow. Though it should not, since these activites run in a parallel thread.
API for non-destrictive plugins
While there are many plugins for Aperture right now, they are working in a destructive way: they copy your image when you use them. That's not so funny if your original RAW image is 14M and the TIFF file from it is also at least that big. I could imagine non-destructive third-party plugins for framing and watermarking, more effects, like adjusting perspective, etc.
No, I don't want Aperture to edit video, just to manage the content which is downloaded from my camera (including video maybe), show a thumbnail, and call the appropriate editing software (iMovie, Final Cut Express, etc.) if necessary. Modern DSLR-s have video support now, and the Canon EOS 5D MkII can be considered a pretty decent full-frame camera.
It has now vault, but it is limited to local drives, and I've heard that it is not really compatible with Time Machine (e.g.: if Aperture is running, then it possibly back up an inconsistent Aperture Library).
Extending the Vault to remote drives would be just simply awesome!
These were the things what I expect in Aperture to be improved. I think these are not too much, no need for fancy new features, just a more solid and faster app.